Multiple sequence alignment - TraesCS3B01G323300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G323300 chr3B 100.000 6135 0 0 1 6135 523145810 523139676 0.000000e+00 11330
1 TraesCS3B01G323300 chr3B 78.417 4207 651 147 1005 5138 69640906 69636884 0.000000e+00 2501
2 TraesCS3B01G323300 chr3A 92.567 6175 332 46 6 6135 516787725 516781633 0.000000e+00 8743
3 TraesCS3B01G323300 chr3A 79.121 2639 400 94 974 3563 56560781 56558245 0.000000e+00 1681
4 TraesCS3B01G323300 chr3D 94.208 4282 219 18 1872 6135 397186097 397181827 0.000000e+00 6506
5 TraesCS3B01G323300 chr3D 92.034 1908 114 21 2 1876 397199370 397197468 0.000000e+00 2647
6 TraesCS3B01G323300 chr4A 83.017 5111 637 149 868 5848 215127023 215132032 0.000000e+00 4416
7 TraesCS3B01G323300 chr4A 82.713 376 48 13 102 471 215125955 215126319 9.920000e-83 318
8 TraesCS3B01G323300 chr4A 79.184 245 37 11 5897 6135 215132132 215132368 2.290000e-34 158
9 TraesCS3B01G323300 chr5A 82.818 5110 645 151 868 5848 604815388 604810383 0.000000e+00 4357
10 TraesCS3B01G323300 chr5A 82.480 5120 651 151 864 5839 555373696 555378713 0.000000e+00 4259
11 TraesCS3B01G323300 chr5A 88.902 1739 150 29 819 2536 644504335 644506051 0.000000e+00 2102
12 TraesCS3B01G323300 chr5A 86.088 726 78 15 101 816 644503400 644504112 0.000000e+00 760
13 TraesCS3B01G323300 chr5A 84.986 726 90 16 101 816 644484931 644485647 0.000000e+00 719
14 TraesCS3B01G323300 chr5A 82.461 382 50 13 102 477 604816456 604816086 9.920000e-83 318
15 TraesCS3B01G323300 chr5A 80.408 245 35 10 5897 6135 604810283 604810046 2.270000e-39 174
16 TraesCS3B01G323300 chr5A 78.367 245 39 10 5897 6135 555378820 555379056 4.960000e-31 147
17 TraesCS3B01G323300 chr2D 84.974 4399 499 105 903 5195 192299025 192294683 0.000000e+00 4313
18 TraesCS3B01G323300 chr2D 78.277 534 82 24 102 620 192300232 192299718 4.620000e-81 313
19 TraesCS3B01G323300 chr2D 81.893 243 35 6 5897 6135 192293876 192293639 4.850000e-46 196
20 TraesCS3B01G323300 chr1D 84.984 3816 429 81 697 4428 2860690 2864445 0.000000e+00 3740
21 TraesCS3B01G323300 chr1D 82.467 827 109 25 4425 5224 2873205 2874022 0.000000e+00 691
22 TraesCS3B01G323300 chr1D 80.220 546 80 21 101 631 2859648 2860180 9.650000e-103 385
23 TraesCS3B01G323300 chr1D 80.408 245 35 9 5897 6135 2881472 2881709 2.270000e-39 174
24 TraesCS3B01G323300 chr6B 84.387 3798 455 84 868 4575 683642802 683639053 0.000000e+00 3602
25 TraesCS3B01G323300 chr6B 78.538 1300 187 65 4589 5848 683638773 683637526 0.000000e+00 771
26 TraesCS3B01G323300 chr6B 82.199 382 51 13 102 477 683643870 683643500 4.620000e-81 313
27 TraesCS3B01G323300 chr6B 80.000 245 36 10 5897 6135 683637426 683637189 1.060000e-37 169
28 TraesCS3B01G323300 chr6D 85.325 2644 303 54 641 3235 439519924 439522531 0.000000e+00 2654
29 TraesCS3B01G323300 chr6D 83.501 2885 325 100 3250 6051 439541502 439544318 0.000000e+00 2551
30 TraesCS3B01G323300 chr7A 86.149 2267 238 51 3055 5297 301167464 301165250 0.000000e+00 2377
31 TraesCS3B01G323300 chr7A 86.303 1650 156 40 544 2164 301249072 301247464 0.000000e+00 1731
32 TraesCS3B01G323300 chr7A 89.691 97 8 1 447 541 301249149 301249053 8.350000e-24 122
33 TraesCS3B01G323300 chr7D 85.280 2269 234 53 3055 5298 271057162 271054969 0.000000e+00 2248
34 TraesCS3B01G323300 chr1A 83.164 2465 306 58 874 3299 5813204 5810810 0.000000e+00 2152
35 TraesCS3B01G323300 chr1A 83.504 2340 303 62 2995 5275 496060132 496062447 0.000000e+00 2106
36 TraesCS3B01G323300 chr1A 78.893 488 62 26 101 577 496056820 496057277 6.010000e-75 292
37 TraesCS3B01G323300 chr1A 76.214 597 94 28 198 780 5814006 5813444 7.840000e-69 272
38 TraesCS3B01G323300 chr5B 85.230 914 115 16 285 1189 97520493 97521395 0.000000e+00 922
39 TraesCS3B01G323300 chr2A 78.439 487 64 25 102 577 571478920 571478464 4.680000e-71 279


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G323300 chr3B 523139676 523145810 6134 True 11330.000000 11330 100.000000 1 6135 1 chr3B.!!$R2 6134
1 TraesCS3B01G323300 chr3B 69636884 69640906 4022 True 2501.000000 2501 78.417000 1005 5138 1 chr3B.!!$R1 4133
2 TraesCS3B01G323300 chr3A 516781633 516787725 6092 True 8743.000000 8743 92.567000 6 6135 1 chr3A.!!$R2 6129
3 TraesCS3B01G323300 chr3A 56558245 56560781 2536 True 1681.000000 1681 79.121000 974 3563 1 chr3A.!!$R1 2589
4 TraesCS3B01G323300 chr3D 397181827 397186097 4270 True 6506.000000 6506 94.208000 1872 6135 1 chr3D.!!$R1 4263
5 TraesCS3B01G323300 chr3D 397197468 397199370 1902 True 2647.000000 2647 92.034000 2 1876 1 chr3D.!!$R2 1874
6 TraesCS3B01G323300 chr4A 215125955 215132368 6413 False 1630.666667 4416 81.638000 102 6135 3 chr4A.!!$F1 6033
7 TraesCS3B01G323300 chr5A 555373696 555379056 5360 False 2203.000000 4259 80.423500 864 6135 2 chr5A.!!$F2 5271
8 TraesCS3B01G323300 chr5A 604810046 604816456 6410 True 1616.333333 4357 81.895667 102 6135 3 chr5A.!!$R1 6033
9 TraesCS3B01G323300 chr5A 644503400 644506051 2651 False 1431.000000 2102 87.495000 101 2536 2 chr5A.!!$F3 2435
10 TraesCS3B01G323300 chr5A 644484931 644485647 716 False 719.000000 719 84.986000 101 816 1 chr5A.!!$F1 715
11 TraesCS3B01G323300 chr2D 192293639 192300232 6593 True 1607.333333 4313 81.714667 102 6135 3 chr2D.!!$R1 6033
12 TraesCS3B01G323300 chr1D 2859648 2864445 4797 False 2062.500000 3740 82.602000 101 4428 2 chr1D.!!$F3 4327
13 TraesCS3B01G323300 chr1D 2873205 2874022 817 False 691.000000 691 82.467000 4425 5224 1 chr1D.!!$F1 799
14 TraesCS3B01G323300 chr6B 683637189 683643870 6681 True 1213.750000 3602 81.281000 102 6135 4 chr6B.!!$R1 6033
15 TraesCS3B01G323300 chr6D 439519924 439522531 2607 False 2654.000000 2654 85.325000 641 3235 1 chr6D.!!$F1 2594
16 TraesCS3B01G323300 chr6D 439541502 439544318 2816 False 2551.000000 2551 83.501000 3250 6051 1 chr6D.!!$F2 2801
17 TraesCS3B01G323300 chr7A 301165250 301167464 2214 True 2377.000000 2377 86.149000 3055 5297 1 chr7A.!!$R1 2242
18 TraesCS3B01G323300 chr7A 301247464 301249149 1685 True 926.500000 1731 87.997000 447 2164 2 chr7A.!!$R2 1717
19 TraesCS3B01G323300 chr7D 271054969 271057162 2193 True 2248.000000 2248 85.280000 3055 5298 1 chr7D.!!$R1 2243
20 TraesCS3B01G323300 chr1A 5810810 5814006 3196 True 1212.000000 2152 79.689000 198 3299 2 chr1A.!!$R1 3101
21 TraesCS3B01G323300 chr1A 496056820 496062447 5627 False 1199.000000 2106 81.198500 101 5275 2 chr1A.!!$F1 5174
22 TraesCS3B01G323300 chr5B 97520493 97521395 902 False 922.000000 922 85.230000 285 1189 1 chr5B.!!$F1 904

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
430 484 1.001760 AGCCGCTTCTCCCTTCCTA 59.998 57.895 0.00 0.0 0.00 2.94 F
1067 2493 0.179150 TTCGCAACAAAACGCTTGCT 60.179 45.000 4.82 0.0 40.59 3.91 F
1570 3030 0.543749 GGTCATGGGTGCTCTTAGCT 59.456 55.000 0.00 0.0 42.97 3.32 F
2396 3918 1.005450 AGCAACCCAACGGATAATGGT 59.995 47.619 0.00 0.0 34.79 3.55 F
4021 5673 0.179043 TGTTGCTCCCGTTTAGTGCA 60.179 50.000 0.00 0.0 0.00 4.57 F
4143 5812 2.243736 TCCACCCAGAAGTTTTTGACCT 59.756 45.455 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 3928 2.226437 GCGAACCACACACATCTTCATT 59.774 45.455 0.0 0.0 0.00 2.57 R
2559 4114 2.673368 CGTCAGAAGGGATGCAACTTAC 59.327 50.000 0.0 0.0 0.00 2.34 R
3116 4731 2.161855 GCACATCACTCCAATGTCCAA 58.838 47.619 0.0 0.0 35.19 3.53 R
4143 5812 1.942657 GCTCTCTTGCACAAACACTCA 59.057 47.619 0.0 0.0 0.00 3.41 R
5034 7061 2.286294 GTCTTCCGCACATCAAGCATAG 59.714 50.000 0.0 0.0 0.00 2.23 R
6034 8320 1.134580 AGTCGAGGGACATGCTCAATG 60.135 52.381 0.0 0.0 45.92 2.82 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.802507 GCGTGCCCTGCGTATTTA 58.197 55.556 0.00 0.00 0.00 1.40
58 59 3.632145 CCCTGCGTATTTATTTTGCTCCT 59.368 43.478 0.00 0.00 0.00 3.69
82 83 3.063084 GTGAGCTCGGTCGTCCCT 61.063 66.667 9.64 0.00 0.00 4.20
83 84 2.750637 TGAGCTCGGTCGTCCCTC 60.751 66.667 9.64 0.00 0.00 4.30
90 91 2.579738 GGTCGTCCCTCCTGCTTC 59.420 66.667 0.00 0.00 0.00 3.86
98 99 2.761465 CCTCCTGCTTCCATCCCCC 61.761 68.421 0.00 0.00 0.00 5.40
120 144 3.148279 AGGCGACCCGAGATCCAC 61.148 66.667 0.00 0.00 35.76 4.02
137 162 4.402528 CAATCGTGGTGGGGCGGA 62.403 66.667 0.00 0.00 0.00 5.54
148 173 2.506472 GGGCGGAGGAACTGGATC 59.494 66.667 0.00 0.00 41.55 3.36
224 249 4.111016 CGCCGAGCTACACGACCA 62.111 66.667 0.00 0.00 0.00 4.02
386 440 6.882678 TCGGGTCGAATTCATAGTATAGATGA 59.117 38.462 6.22 0.00 31.06 2.92
419 473 1.172812 GGGTTTCAGTTGAGCCGCTT 61.173 55.000 0.00 0.00 0.00 4.68
430 484 1.001760 AGCCGCTTCTCCCTTCCTA 59.998 57.895 0.00 0.00 0.00 2.94
471 528 1.975660 TCACCTAGGGTTTGTTGTGC 58.024 50.000 14.81 0.00 31.02 4.57
535 602 5.959583 AGTTGAGATTTTAGAGGTAGGGG 57.040 43.478 0.00 0.00 0.00 4.79
536 603 5.600749 AGTTGAGATTTTAGAGGTAGGGGA 58.399 41.667 0.00 0.00 0.00 4.81
537 604 5.425862 AGTTGAGATTTTAGAGGTAGGGGAC 59.574 44.000 0.00 0.00 0.00 4.46
538 605 3.958798 TGAGATTTTAGAGGTAGGGGACG 59.041 47.826 0.00 0.00 0.00 4.79
539 606 4.213513 GAGATTTTAGAGGTAGGGGACGA 58.786 47.826 0.00 0.00 0.00 4.20
540 607 4.216708 AGATTTTAGAGGTAGGGGACGAG 58.783 47.826 0.00 0.00 0.00 4.18
541 608 3.463048 TTTTAGAGGTAGGGGACGAGT 57.537 47.619 0.00 0.00 0.00 4.18
542 609 3.463048 TTTAGAGGTAGGGGACGAGTT 57.537 47.619 0.00 0.00 0.00 3.01
543 610 3.463048 TTAGAGGTAGGGGACGAGTTT 57.537 47.619 0.00 0.00 0.00 2.66
589 1213 5.584913 TCAGAGTTGGAGGACTAGATTCTT 58.415 41.667 0.00 0.00 0.00 2.52
639 1782 7.558444 TGTTTGGTTAGTCAAGTTATGGTTTCT 59.442 33.333 0.00 0.00 0.00 2.52
692 1869 9.778741 TTTTTAGATGAAAGTCAGTGTAGTCAT 57.221 29.630 0.00 0.00 0.00 3.06
915 2326 6.326323 TGGTAGATGTTGAGTATGCTGGAATA 59.674 38.462 0.00 0.00 0.00 1.75
933 2344 4.432712 GAATACAAATGCCCATCGCTTTT 58.567 39.130 0.00 0.00 43.55 2.27
960 2382 8.391859 TGTAGTAATTGTATAATGGCGTTTGTG 58.608 33.333 0.00 0.00 0.00 3.33
1003 2427 7.153315 TCATTTTGATTTTTGCAGCTACATGA 58.847 30.769 0.00 0.00 0.00 3.07
1024 2448 3.851098 ACAGACGAAGAAGTAATGGAGC 58.149 45.455 0.00 0.00 0.00 4.70
1032 2456 4.965200 AGAAGTAATGGAGCCTGATACC 57.035 45.455 0.00 0.00 0.00 2.73
1035 2459 2.365617 AGTAATGGAGCCTGATACCGTG 59.634 50.000 0.00 0.00 0.00 4.94
1054 2480 1.199327 TGTTCAACCAACGTTTCGCAA 59.801 42.857 0.00 0.00 37.90 4.85
1067 2493 0.179150 TTCGCAACAAAACGCTTGCT 60.179 45.000 4.82 0.00 40.59 3.91
1155 2581 4.564782 TCTCATGAGCATCTCACCTTTT 57.435 40.909 18.36 0.00 43.63 2.27
1191 2617 8.685427 CATGATTTGATGGAGTGGTTAACAATA 58.315 33.333 8.10 0.00 0.00 1.90
1354 2813 2.550180 GGTTTTCAGGCTGAGTCAGAAC 59.450 50.000 24.55 16.28 32.44 3.01
1570 3030 0.543749 GGTCATGGGTGCTCTTAGCT 59.456 55.000 0.00 0.00 42.97 3.32
1702 3169 3.498774 AGTGTTGCAATGAGAGAGGTT 57.501 42.857 0.59 0.00 0.00 3.50
2011 3504 3.694072 TCTTGTGTTGGACTTTGACAAGG 59.306 43.478 0.00 0.00 42.42 3.61
2028 3521 4.998051 ACAAGGATAAGCTTTCTTTGGGA 58.002 39.130 23.77 2.23 35.25 4.37
2037 3530 2.630098 GCTTTCTTTGGGAAAAGCCTCT 59.370 45.455 8.29 0.00 42.52 3.69
2135 3644 7.707774 TTTACCTTCTTATTTTTGCTTGTGC 57.292 32.000 0.00 0.00 40.20 4.57
2211 3725 1.067846 TGTCAGAGACACCATACGCAC 60.068 52.381 0.00 0.00 37.67 5.34
2301 3815 3.273434 CCGGATTGTGATGACACTCAAT 58.727 45.455 0.00 0.00 46.07 2.57
2396 3918 1.005450 AGCAACCCAACGGATAATGGT 59.995 47.619 0.00 0.00 34.79 3.55
2510 4035 9.635520 TTTTTGTGTTTCTATTTCCGTTGTTTA 57.364 25.926 0.00 0.00 0.00 2.01
2511 4036 9.635520 TTTTGTGTTTCTATTTCCGTTGTTTAA 57.364 25.926 0.00 0.00 0.00 1.52
2574 4129 5.387113 TCATATGGTAAGTTGCATCCCTT 57.613 39.130 2.13 0.00 0.00 3.95
2637 4201 3.450817 TCCCATCACACATCTACGACAAT 59.549 43.478 0.00 0.00 0.00 2.71
2682 4246 4.576879 AGTTAAAAGGGGCTCTAAGTTCG 58.423 43.478 0.00 0.00 0.00 3.95
2866 4436 4.263112 GCAAGGAAAGTTCTAGGGAGAAGT 60.263 45.833 0.00 0.00 45.60 3.01
2987 4557 1.073722 TTGAGCTGGGCACAGGAAG 59.926 57.895 19.71 0.00 45.04 3.46
3014 4629 2.917933 TGTTGTCAGTGAGAACCTTGG 58.082 47.619 25.47 0.00 35.38 3.61
3036 4651 4.320494 GGACGATGTTTTGAGACTGCAAAT 60.320 41.667 0.00 0.00 37.57 2.32
3116 4731 0.826256 TCTGTGCCGACTAGTGTGGT 60.826 55.000 0.00 0.00 0.00 4.16
3170 4785 2.045536 CCAAGAGGGCACTGAGGC 60.046 66.667 0.00 0.00 43.27 4.70
3589 5224 2.668632 GGAGTCCAATGTCGGCCA 59.331 61.111 3.60 0.00 0.00 5.36
3598 5233 1.098050 AATGTCGGCCAGATCAAAGC 58.902 50.000 2.24 0.00 0.00 3.51
3617 5253 4.843220 AGCACAAGAAAATCAAGACAGG 57.157 40.909 0.00 0.00 0.00 4.00
3909 5558 3.607422 TGCAACGAAGTCATGTCTTTG 57.393 42.857 15.78 15.78 45.00 2.77
3942 5591 6.219417 ACCTTCAACATTGAACAATTGTCA 57.781 33.333 12.39 8.91 41.88 3.58
4012 5664 1.734465 GTTCATCTCTTGTTGCTCCCG 59.266 52.381 0.00 0.00 0.00 5.14
4021 5673 0.179043 TGTTGCTCCCGTTTAGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
4032 5684 5.941058 TCCCGTTTAGTGCAATCATTTTCTA 59.059 36.000 0.00 0.00 0.00 2.10
4033 5685 6.093495 TCCCGTTTAGTGCAATCATTTTCTAG 59.907 38.462 0.00 0.00 0.00 2.43
4036 5688 7.148407 CCGTTTAGTGCAATCATTTTCTAGAGT 60.148 37.037 0.00 0.00 0.00 3.24
4141 5810 3.020984 TGTCCACCCAGAAGTTTTTGAC 58.979 45.455 0.00 0.00 0.00 3.18
4143 5812 2.243736 TCCACCCAGAAGTTTTTGACCT 59.756 45.455 0.00 0.00 0.00 3.85
4428 6105 5.478679 TGGATAACGGAAAATTGGATGTTGT 59.521 36.000 0.00 0.00 0.00 3.32
4441 6118 4.661222 TGGATGTTGTTGCAAGGAATCTA 58.339 39.130 0.00 0.00 0.00 1.98
4644 6629 4.276926 CCACTATTTCCTATTTCTGCCAGC 59.723 45.833 0.00 0.00 0.00 4.85
4743 6728 3.576982 CCTACTTGACTACCCACAACAGA 59.423 47.826 0.00 0.00 0.00 3.41
4761 6746 3.505680 ACAGACAACTCAGTGAGCTCTAG 59.494 47.826 20.31 12.90 32.04 2.43
4767 6752 3.696045 ACTCAGTGAGCTCTAGTCACAT 58.304 45.455 20.31 0.00 45.76 3.21
4769 6754 4.638421 ACTCAGTGAGCTCTAGTCACATAC 59.362 45.833 20.31 0.83 45.76 2.39
5034 7061 5.803967 CCAATTTCTCTCTTATGCAGCAAAC 59.196 40.000 0.00 0.00 0.00 2.93
5310 7354 6.425735 TCTATTTGGCTGGAATGATTCTCAA 58.574 36.000 5.03 3.14 0.00 3.02
5389 7436 1.468395 CGTGTGGTGGTTTGTTGGAAC 60.468 52.381 0.00 0.00 0.00 3.62
5410 7457 6.431852 GGAACCAAGTTATACCAGTTTTGCTA 59.568 38.462 0.00 0.00 0.00 3.49
5443 7491 7.979537 ACTCAACCTTTTCAAGTTTTATGGAAC 59.020 33.333 0.00 0.00 0.00 3.62
5466 7515 8.515473 AACACTTCTCAGTTTTTGTTACAAAC 57.485 30.769 10.28 0.79 34.80 2.93
5585 7641 3.130516 AGGAAGCATGCTCATGAAACATG 59.869 43.478 22.93 24.33 43.21 3.21
5702 7924 4.332268 GCTTCCTAGAACAAGCATTCTCAG 59.668 45.833 13.28 0.00 43.87 3.35
5703 7925 5.486526 CTTCCTAGAACAAGCATTCTCAGT 58.513 41.667 1.58 0.00 39.65 3.41
5823 8050 4.517453 TCTCTTAATTCCCCACAAAACACG 59.483 41.667 0.00 0.00 0.00 4.49
5874 8109 3.691118 TCACTTCTGCAGCAATATCAACC 59.309 43.478 9.47 0.00 0.00 3.77
5882 8117 4.766373 TGCAGCAATATCAACCTTTTGAGA 59.234 37.500 0.00 0.00 45.07 3.27
5960 8241 7.226720 ACAGAAAATTCAGTAACACTACACAGG 59.773 37.037 0.00 0.00 0.00 4.00
6034 8320 6.049149 TGAACTGCAGCAGTATAATCTAACC 58.951 40.000 28.48 8.09 44.62 2.85
6060 8346 0.108615 CATGTCCCTCGACTTTCGCT 60.109 55.000 0.00 0.00 40.21 4.93
6061 8347 0.108615 ATGTCCCTCGACTTTCGCTG 60.109 55.000 0.00 0.00 40.21 5.18
6065 8351 0.600255 CCCTCGACTTTCGCTGTTGT 60.600 55.000 0.00 0.00 40.21 3.32
6119 8405 1.443802 CCTTCCTCGGAGCAAAACTC 58.556 55.000 0.00 0.00 45.45 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.023450 GGGGTAGGAGCAAAATAAATACGC 60.023 45.833 0.00 0.00 0.00 4.42
41 42 4.517832 GGGGGTAGGAGCAAAATAAATACG 59.482 45.833 0.00 0.00 0.00 3.06
48 49 0.034477 CACGGGGGTAGGAGCAAAAT 60.034 55.000 0.00 0.00 0.00 1.82
99 100 3.781770 GATCTCGGGTCGCCTGCAG 62.782 68.421 6.78 6.78 0.00 4.41
120 144 4.402528 TCCGCCCCACCACGATTG 62.403 66.667 0.00 0.00 0.00 2.67
129 153 3.943137 ATCCAGTTCCTCCGCCCCA 62.943 63.158 0.00 0.00 0.00 4.96
148 173 2.046892 CCTTGTCGTCCCTGCAGG 60.047 66.667 26.87 26.87 0.00 4.85
224 249 4.388499 CCGCCGCAACTACAGGGT 62.388 66.667 0.00 0.00 0.00 4.34
361 411 6.882678 TCATCTATACTATGAATTCGACCCGA 59.117 38.462 0.04 0.00 30.52 5.14
386 440 3.436243 TGAAACCCCTGAACAAACAACT 58.564 40.909 0.00 0.00 0.00 3.16
419 473 0.545787 TTTGGCGGTAGGAAGGGAGA 60.546 55.000 0.00 0.00 0.00 3.71
430 484 1.381191 GGGGGATGAATTTGGCGGT 60.381 57.895 0.00 0.00 0.00 5.68
471 528 8.004087 ACATGGAACCAAATTAATCTGATCTG 57.996 34.615 0.00 0.00 0.00 2.90
523 590 3.463048 AAACTCGTCCCCTACCTCTAA 57.537 47.619 0.00 0.00 0.00 2.10
524 591 3.463048 AAAACTCGTCCCCTACCTCTA 57.537 47.619 0.00 0.00 0.00 2.43
525 592 2.322339 AAAACTCGTCCCCTACCTCT 57.678 50.000 0.00 0.00 0.00 3.69
542 609 9.009675 TGAAATCTCATCCCCTACCTATAAAAA 57.990 33.333 0.00 0.00 0.00 1.94
543 610 8.575736 TGAAATCTCATCCCCTACCTATAAAA 57.424 34.615 0.00 0.00 0.00 1.52
639 1782 9.073475 ACCTAATCTAAACAACAAATACAGCAA 57.927 29.630 0.00 0.00 0.00 3.91
780 1960 4.624015 CATGACACAACCAGCTCAAAAAT 58.376 39.130 0.00 0.00 0.00 1.82
915 2326 2.415776 CAAAAAGCGATGGGCATTTGT 58.584 42.857 0.00 0.00 41.33 2.83
933 2344 8.948145 ACAAACGCCATTATACAATTACTACAA 58.052 29.630 0.00 0.00 0.00 2.41
1003 2427 3.368531 GGCTCCATTACTTCTTCGTCTGT 60.369 47.826 0.00 0.00 0.00 3.41
1024 2448 2.465860 TGGTTGAACACGGTATCAGG 57.534 50.000 0.00 0.00 0.00 3.86
1032 2456 1.448722 CGAAACGTTGGTTGAACACG 58.551 50.000 0.00 6.64 36.25 4.49
1035 2459 1.580256 GTTGCGAAACGTTGGTTGAAC 59.420 47.619 0.00 0.00 36.25 3.18
1054 2480 1.014352 ACTTCGAGCAAGCGTTTTGT 58.986 45.000 4.21 0.00 35.17 2.83
1067 2493 2.933906 AGTTTTGTCTTCGCAACTTCGA 59.066 40.909 0.00 0.00 36.60 3.71
1109 2535 3.119495 ACCGAAGCCAGTTTCATTTATGC 60.119 43.478 0.00 0.00 0.00 3.14
1155 2581 3.752747 CCATCAAATCATGTGGCGCTATA 59.247 43.478 7.64 0.00 0.00 1.31
1191 2617 5.113383 TCACGACTGTTAGTGTCAATGTTT 58.887 37.500 14.09 0.00 39.25 2.83
1354 2813 4.988540 TCTCGAGTAAACACAATGACCTTG 59.011 41.667 13.13 0.00 40.90 3.61
1570 3030 5.678616 GCTTGGAGTTAAAACTGTTGCAAGA 60.679 40.000 14.67 0.00 39.88 3.02
1702 3169 5.755409 TTATCTTGTCCTGGCACTTCTTA 57.245 39.130 0.00 0.00 0.00 2.10
2011 3504 5.047021 AGGCTTTTCCCAAAGAAAGCTTATC 60.047 40.000 17.16 0.00 45.11 1.75
2028 3521 3.374764 ACACTTCCCAAAAGAGGCTTTT 58.625 40.909 0.00 0.00 0.00 2.27
2037 3530 3.876341 ACTTACACGACACTTCCCAAAA 58.124 40.909 0.00 0.00 0.00 2.44
2135 3644 9.533253 AAGAAACAAGAATTAAAACCATGAGTG 57.467 29.630 0.00 0.00 0.00 3.51
2301 3815 6.662755 AGTTGATATTTCCAGCTCCACAATA 58.337 36.000 0.00 0.00 0.00 1.90
2396 3918 5.301551 ACACACATCTTCATTGGTGCTTTTA 59.698 36.000 0.00 0.00 34.69 1.52
2406 3928 2.226437 GCGAACCACACACATCTTCATT 59.774 45.455 0.00 0.00 0.00 2.57
2501 4026 8.582433 AAAGGTATTTGACAATTAAACAACGG 57.418 30.769 0.00 0.00 0.00 4.44
2502 4027 9.458374 AGAAAGGTATTTGACAATTAAACAACG 57.542 29.630 0.00 0.00 0.00 4.10
2511 4036 9.588096 AGAAAAGGTAGAAAGGTATTTGACAAT 57.412 29.630 0.00 0.00 0.00 2.71
2559 4114 2.673368 CGTCAGAAGGGATGCAACTTAC 59.327 50.000 0.00 0.00 0.00 2.34
2625 4180 6.228273 AGTTTTGTGTGATTGTCGTAGATG 57.772 37.500 0.00 0.00 40.67 2.90
2637 4201 8.109705 ACTTTGCATCATATAGTTTTGTGTGA 57.890 30.769 0.00 0.00 0.00 3.58
2717 4281 3.079578 TCTTTGAGAAGCTGCTCCATTG 58.920 45.455 19.57 6.97 33.95 2.82
2866 4436 3.006430 TCAGTTGTTGGCTCATCTACGAA 59.994 43.478 0.00 0.00 0.00 3.85
2987 4557 4.270325 GGTTCTCACTGACAACAACACTAC 59.730 45.833 0.35 0.00 0.00 2.73
3014 4629 3.878086 TTGCAGTCTCAAAACATCGTC 57.122 42.857 0.00 0.00 0.00 4.20
3036 4651 6.911250 TCTTCACCACTAGACACTTTATCA 57.089 37.500 0.00 0.00 0.00 2.15
3116 4731 2.161855 GCACATCACTCCAATGTCCAA 58.838 47.619 0.00 0.00 35.19 3.53
3170 4785 4.758674 GGACACTGATCCACCAATCATATG 59.241 45.833 0.00 0.00 38.77 1.78
3534 5169 3.322254 TCTTGAGCTTCTTCTCGTCCTTT 59.678 43.478 0.00 0.00 35.90 3.11
3589 5224 7.144000 GTCTTGATTTTCTTGTGCTTTGATCT 58.856 34.615 0.00 0.00 0.00 2.75
3598 5233 5.007626 TCGAACCTGTCTTGATTTTCTTGTG 59.992 40.000 0.00 0.00 0.00 3.33
3617 5253 4.201822 GGTACATTGCTTCCATCTTCGAAC 60.202 45.833 0.00 0.00 0.00 3.95
3757 5398 3.460857 AGGAGCGTTTGATAGGATGAC 57.539 47.619 0.00 0.00 0.00 3.06
3763 5406 7.085116 CCATAGTAGTTAGGAGCGTTTGATAG 58.915 42.308 0.00 0.00 0.00 2.08
3909 5558 5.757886 TCAATGTTGAAGGTTTCGATGAAC 58.242 37.500 0.00 0.00 33.55 3.18
3942 5591 9.148104 GCAAATTTCTTCTGCTTATTTGAAGAT 57.852 29.630 0.00 0.00 43.52 2.40
4012 5664 9.899226 AAACTCTAGAAAATGATTGCACTAAAC 57.101 29.630 0.00 0.00 0.00 2.01
4042 5694 7.054124 TGGAGAACTTTGTAATAGGGCATAAG 58.946 38.462 0.00 0.00 0.00 1.73
4055 5712 7.410120 AAGAAAAAGTGATGGAGAACTTTGT 57.590 32.000 1.86 0.00 43.92 2.83
4056 5713 9.403110 CATAAGAAAAAGTGATGGAGAACTTTG 57.597 33.333 1.86 0.00 43.92 2.77
4141 5810 2.547211 CTCTCTTGCACAAACACTCAGG 59.453 50.000 0.00 0.00 0.00 3.86
4143 5812 1.942657 GCTCTCTTGCACAAACACTCA 59.057 47.619 0.00 0.00 0.00 3.41
4301 5974 9.684448 GAAGAAAAGCTAGAAAAAGCAGTAAAT 57.316 29.630 0.00 0.00 45.30 1.40
4428 6105 6.109156 TGTCACTTACTAGATTCCTTGCAA 57.891 37.500 0.00 0.00 0.00 4.08
4532 6226 5.582269 ACTTCATACACATTCGGATTCACTG 59.418 40.000 0.00 0.00 0.00 3.66
4626 6609 4.889995 GGTAAGCTGGCAGAAATAGGAAAT 59.110 41.667 20.86 0.00 0.00 2.17
4644 6629 6.521151 AGCAATCCTCTTGAAATTGGTAAG 57.479 37.500 7.74 0.00 38.82 2.34
4743 6728 3.254657 GTGACTAGAGCTCACTGAGTTGT 59.745 47.826 17.77 0.51 35.99 3.32
5034 7061 2.286294 GTCTTCCGCACATCAAGCATAG 59.714 50.000 0.00 0.00 0.00 2.23
5120 7149 4.997395 TCACTTTCTTCAAGCCACTATGAC 59.003 41.667 0.00 0.00 35.65 3.06
5152 7182 3.575256 TGCTGCAATCACCTTCTTCAATT 59.425 39.130 0.00 0.00 0.00 2.32
5164 7194 4.552355 CATCTTCAAAACTGCTGCAATCA 58.448 39.130 3.02 0.00 0.00 2.57
5389 7436 7.305474 CAAGTAGCAAAACTGGTATAACTTGG 58.695 38.462 9.18 0.00 0.00 3.61
5399 7446 4.385825 TGAGTACCAAGTAGCAAAACTGG 58.614 43.478 0.00 0.00 0.00 4.00
5410 7457 5.949952 AACTTGAAAAGGTTGAGTACCAAGT 59.050 36.000 0.00 0.00 45.56 3.16
5443 7491 6.799925 ACGTTTGTAACAAAAACTGAGAAGTG 59.200 34.615 0.00 0.00 35.75 3.16
5444 7492 6.905578 ACGTTTGTAACAAAAACTGAGAAGT 58.094 32.000 0.00 0.00 35.75 3.01
5466 7515 5.741510 TGCTAGAAAAACACACATGAAAACG 59.258 36.000 0.00 0.00 0.00 3.60
5615 7675 5.769662 TCTTCCAGCAACAATTATCACAAGT 59.230 36.000 0.00 0.00 0.00 3.16
5683 7905 6.566197 AAAACTGAGAATGCTTGTTCTAGG 57.434 37.500 0.00 0.79 38.51 3.02
5850 8077 4.476628 TGATATTGCTGCAGAAGTGAGA 57.523 40.909 20.43 0.00 0.00 3.27
5933 8213 8.500753 TGTGTAGTGTTACTGAATTTTCTGTT 57.499 30.769 7.93 0.00 39.57 3.16
5982 8266 8.023021 TCATGTATCAGTAACTTGAAGCCTAT 57.977 34.615 0.00 0.00 30.64 2.57
6034 8320 1.134580 AGTCGAGGGACATGCTCAATG 60.135 52.381 0.00 0.00 45.92 2.82
6060 8346 4.824537 TGCATCCAGTTTAAAGCTACAACA 59.175 37.500 0.00 0.00 0.00 3.33
6061 8347 5.371115 TGCATCCAGTTTAAAGCTACAAC 57.629 39.130 0.00 0.00 0.00 3.32
6065 8351 6.798482 CAATCATGCATCCAGTTTAAAGCTA 58.202 36.000 0.00 0.00 0.00 3.32


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.